diff --git a/docs/src/.gitignore b/docs/src/.gitignore index 269ce7da..35be25fd 100644 --- a/docs/src/.gitignore +++ b/docs/src/.gitignore @@ -1 +1,2 @@ sg_execution_times.rst +all-examples.rst diff --git a/docs/src/conf.py b/docs/src/conf.py index a4a11fcd..6847db9e 100644 --- a/docs/src/conf.py +++ b/docs/src/conf.py @@ -5,7 +5,6 @@ # Add any Sphinx extension module names here, as strings. extensions = [ "sphinx_sitemap", - "sphinx_design", "sphinx.ext.viewcode", "sphinx.ext.intersphinx", "sphinx_gallery.load_style", @@ -34,7 +33,7 @@ html_js_files = [ ( # plausible.io tracking - "https://plausible.io/js/script.file-downloads.hash.outbound-links.pageview-props.tagged-events.js", + "https://plausible.io/js/script.file-downloads.hash.outbound-links.pageview-props.tagged-events.js", # noqa: E501 {"data-domain": "atomistic-cookbook.org", "defer": "defer"}, ), ] diff --git a/docs/src/index.rst b/docs/src/index.rst index f79afced..40d3e048 100644 --- a/docs/src/index.rst +++ b/docs/src/index.rst @@ -16,8 +16,8 @@ then use with conda to create a new environment with all the required dependenci # when you want to use the environment conda env activate --name -Additional data needed for each example is usually either downloaded -dynamically, or can be found in a ``data`` folder for each example, +Additional data needed for each example is usually either downloaded +dynamically, or can be found in a ``data`` folder for each example, or downloaded as a ``data.zip`` file at the end of each recipe in the website. @@ -26,8 +26,8 @@ Table of contents .. toctree:: :maxdepth: 1 - - contributing + topics/index software/index all-examples + contributing diff --git a/docs/src/software/.gitignore b/docs/src/software/.gitignore new file mode 100644 index 00000000..049a3c64 --- /dev/null +++ b/docs/src/software/.gitignore @@ -0,0 +1,2 @@ +*.rst +!index.rst diff --git a/docs/src/software/chemiscope.sec b/docs/src/software/chemiscope.sec index 56175454..360bf713 100644 --- a/docs/src/software/chemiscope.sec +++ b/docs/src/software/chemiscope.sec @@ -3,16 +3,14 @@ chemiscope ========== -Chemiscope is a tool for interactive exploration of databases of -materials and molecules, correlating local and global structural -representations with the properties of the systems. -Chemiscope files can be viewed -`online `_, generated using a -`python library `_ and -used inside jupyter notebooks or sphinx documentations, which -is how it's used in the cookbook examples. -You can check the `documentation `_ and the -`github repository `_. +Chemiscope is a tool for interactive exploration of databases of materials and +molecules, correlating local and global structural representations with the +properties of the systems. Chemiscope files can be viewed `online +`_, generated using a `python library +`_ and used inside jupyter notebooks or +sphinx documentations, which is how it's used in the cookbook examples. You can +check the `documentation `_ and the `github +repository `_. - examples/roy-gch/roy-gch - examples/gaas-map/gaas-map diff --git a/docs/src/software/cp2k.sec b/docs/src/software/cp2k.sec index c3927dab..924b9fde 100644 --- a/docs/src/software/cp2k.sec +++ b/docs/src/software/cp2k.sec @@ -1,10 +1,9 @@ cp2k ==== -CP2K is a quantum chemistry and solid state physics software package -that can perform atomistic simulations of solid state, liquid, -molecular, periodic, material, crystal, and biological systems. -Learn more about it on its -`homepage `_. +CP2K is a quantum chemistry and solid state physics software package that can +perform atomistic simulations of solid state, liquid, molecular, periodic, +material, crystal, and biological systems. Learn more about it on its `homepage +`_. - examples/batch-cp2k/reference-trajectory diff --git a/docs/src/software/i-pi.sec b/docs/src/software/i-pi.sec index 530c43cd..210b860a 100644 --- a/docs/src/software/i-pi.sec +++ b/docs/src/software/i-pi.sec @@ -1,13 +1,12 @@ i-PI ==== -i-PI is a universal force engine interface written in Python, -designed to be used together with an ab-initio, machine-learned, -or force-field based evaluation of the interactions between the -atoms. You can see learn more about it on the -`ipi-code website `_, the -`documentation pages `_ or -`the github repository `_. +i-PI is a universal force engine interface written in Python, designed to be +used together with an ab-initio, machine-learned, or force-field based +evaluation of the interactions between the atoms. You can see learn more about +it on the `ipi-code website `_, the `documentation pages +`_ or `the github repository +`_. - examples/path-integrals/path-integrals diff --git a/docs/src/software/lammps.sec b/docs/src/software/lammps.sec index 8388c11a..3da23643 100644 --- a/docs/src/software/lammps.sec +++ b/docs/src/software/lammps.sec @@ -1,13 +1,11 @@ LAMMPS ====== -LAMMPS is a classical molecular dynamics (MD) code, with a -focus on materials simulations. It includes a wealth of interatomic -potentials, and of basic and advanced molecular simulations -techniques, and is highly parallelized using an efficient -domain decomposition scheme. -Learn more about LAMMPS on its -`homepage `_. +LAMMPS is a classical molecular dynamics (MD) code, with a focus on materials +simulations. It includes a wealth of interatomic potentials, and of basic and +advanced molecular simulations techniques, and is highly parallelized using an +efficient domain decomposition scheme. Learn more about LAMMPS on its `homepage +`_. - examples/path-integrals/path-integrals - examples/heat-capacity/heat-capacity diff --git a/docs/src/software/plumed.sec b/docs/src/software/plumed.sec index f9786855..3972497c 100644 --- a/docs/src/software/plumed.sec +++ b/docs/src/software/plumed.sec @@ -1,15 +1,13 @@ PLUMED ====== -PLUMED is an open-source, community-developed library that provides -a wide range of different methods, which include enhanced-sampling -algorithms, free-energy methods, tools to analyze the vast amounts -of data produced by molecular dynamics (MD) simulations. -These techniques can be used in combination with a large toolbox of -collective variables that describe complex processes in physics, -chemistry, material science, and biology. -Documentation, examples and installation instructions for the various -packages are discussed on the -`PLUMED website `_. +PLUMED is an open-source, community-developed library that provides a wide range +of different methods, which include enhanced-sampling algorithms, free-energy +methods, tools to analyze the vast amounts of data produced by molecular +dynamics (MD) simulations. These techniques can be used in combination with a +large toolbox of collective variables that describe complex processes in +physics, chemistry, material science, and biology. Documentation, examples and +installation instructions for the various packages are discussed on the `PLUMED +website `_. - examples/pi-metad/pi-metad diff --git a/docs/src/software/rascaline.sec b/docs/src/software/rascaline.sec index 190ddad4..cfd34e86 100644 --- a/docs/src/software/rascaline.sec +++ b/docs/src/software/rascaline.sec @@ -1,14 +1,12 @@ rascaline ========= -Rascaline is a library for the efficient computing of representations -for atomistic machine learning also called “descriptors” or “fingerprints”. -These representation can be used for atomistic machine learning (ML) models -including ML potentials, visualization or similarity analysis. -You can learn how to use it reading the -`documentation `_, and get the latest -version from the -`github repository `_ +Rascaline is a library for the efficient computing of representations for +atomistic machine learning also called “descriptors” or “fingerprints”. These +representation can be used for atomistic machine learning (ML) models including +ML potentials, visualization or similarity analysis. You can learn how to use it +reading the `documentation `_, and get the latest +version from the `github repository `_ - examples/gaas-map/gaas-map - examples/lpr/lpr diff --git a/docs/src/software/scikit-matter.sec b/docs/src/software/scikit-matter.sec index 926613e6..b142a929 100644 --- a/docs/src/software/scikit-matter.sec +++ b/docs/src/software/scikit-matter.sec @@ -1,16 +1,14 @@ scikit-matter ============= -scikit-matter is a toolbox of methods developed in the computational chemical -and materials science community, following the scikit-learn API and coding +scikit-matter is a toolbox of methods developed in the computational chemical +and materials science community, following the scikit-learn API and coding guidelines to promote usability and interoperability with existing workflows. -You can get the latest version from its -`github repository `_ -and learn how to use it from its -`documentation `_. +You can get the latest version from its `github repository +`_ and learn how to use +it from its `documentation `_. - examples/sample-selection/sample-selection - examples/roy-gch/roy-gch - examples/lpr/lpr - examples/gaas-map/gaas-map - diff --git a/docs/src/topics/.gitignore b/docs/src/topics/.gitignore new file mode 100644 index 00000000..049a3c64 --- /dev/null +++ b/docs/src/topics/.gitignore @@ -0,0 +1,2 @@ +*.rst +!index.rst diff --git a/docs/src/topics/ml-models.sec b/docs/src/topics/ml-models.sec index ecb75983..f1cc9954 100644 --- a/docs/src/topics/ml-models.sec +++ b/docs/src/topics/ml-models.sec @@ -1,9 +1,9 @@ Machine learning models ======================= -This section contains recipes that concern the training of -machine-learning models, or the pre-processing of data to -optimize the model architecture or data. +This section contains recipes that concern the training of machine-learning +models, or the pre-processing of data to optimize the model architecture or +data. - examples/dos-align/dos-align - examples/lode-linear/lode-linear diff --git a/docs/src/topics/nqes.sec b/docs/src/topics/nqes.sec index 604f9071..e4dc826e 100644 --- a/docs/src/topics/nqes.sec +++ b/docs/src/topics/nqes.sec @@ -1,11 +1,10 @@ Nuclear quantum effects ======================= -Most atomistic simulations treat nuclei as classical particles, -that sample a Boltzmann distribuion. This approximation breaks -down for light nuclei (hydrogen above all) and high-frequency -vibrations, requiring more sophisticated statistical sampling -to compute accurate statistical and dynamical properties. +Most atomistic simulations treat nuclei as classical particles, that sample a +Boltzmann distribution. This approximation breaks down for light nuclei +(hydrogen above all) and high-frequency vibrations, requiring more sophisticated +statistical sampling to compute accurate statistical and dynamical properties. - examples/path-integrals/path-integrals - examples/pi-metad/pi-metad diff --git a/docs/src/topics/sampling.sec b/docs/src/topics/sampling.sec index 85fe1776..3cdda29e 100644 --- a/docs/src/topics/sampling.sec +++ b/docs/src/topics/sampling.sec @@ -2,7 +2,7 @@ Statistical sampling and dynamics ================================= This section contains recipes that compute thermodynamic averages by sampling, -evaluates dynamical properties, or otherwise computes the properties of a +evaluates dynamical properties, or otherwise computes the properties of a set of configurations of an atomistic system. - examples/path-integrals/path-integrals diff --git a/examples/gaas-map/gaas-map.py b/examples/gaas-map/gaas-map.py index d317263e..d69133f5 100644 --- a/examples/gaas-map/gaas-map.py +++ b/examples/gaas-map/gaas-map.py @@ -33,6 +33,7 @@ from skmatter.decomposition import PCovR from skmatter.preprocessing import StandardFlexibleScaler + # sphinx_gallery_thumbnail_number = 2 ######################################################################